1. Field of the Invention
The invention relates generally to methods for determining the differences between the molecular interactions of two different mixtures of molecules and identifying ligands specific for molecules of one mixture. The invention also relates to screening methods for one-bead-one-compound combinatorial libraries.
2. Description of Related Art
Combinatorial libraries can be used to study interactions between the molecules of a cell. In particular, the one-bead-one-compound library method (Lam, Kit S. et al. “A new type of synthetic peptide library for identifying ligand-binding activity. ” Nature 354 (1991): 82-84) has been used to create libraries of compounds such as peptides, chemical oligomers, and small molecules directed against targets such as antibodies, proteases, streptavidin and other enzymes, as well as bacteria and whole cells. The screening of a bead library with a target molecule or target mixture of molecules results in the identification of beads, referred to as true positive beads, that have bound the target molecules. The chemical structures of the compounds on the true positive beads can then be identified and the compounds confirmed as ligands for the target molecules. The ligands can then be used to determine the interactions with, and structures of, the target molecules.
There is a need for a method for comparing, and determining the differences between, the molecular interactions of two different mixtures of molecules, in particular, functionally-related molecules derived from normal cells and cancer cells. There is also a need for a method for determining ligands specific for molecules in one of the two mixtures, referred to as the target mixture.
There is also a need for a method for accurately screening a combinatorial library to determine which solid phase supports are true positives. A problem with most existing screening methods, which include the use of enzymes, radionuclides, fluorescent probes, and color dyes, is that they result in some beads, referred to as false positives, that directly bind chemicals or reagents used in the screening process. This problem is significant where millions of beads are being screened, as there may be only a small number of true positive beads among a larger number of false positive beads. Thus, a screening method is needed that will accurately identify a small number of true positive beads out of a large number of false positive beads.